Hello Commanders!
Hopefully, it was just that the target was wanted by the faction that controlled the system (hence being wanted in supercruise), but not wanted where they dropped out due to it being controlled by a different faction.
In either case, you need to scan the ship before firing as scan status does not survive supercruise or hyperspace jump transitions.
All this being said, we have made significant changes to the crime system, so keep an eye out for stuff that looks wrong, and submit bugs if necessary.